Re: [galaxy-dev] Packaging pycurl on toolshed
So far I have been trying to avoid this, but I would like to see packaged pycurl on the toolshed now. This is where my package sits: https://testtoolshed.g2.bx.psu.edu/repository?repository_id=534efefdbab02103 and this is the error: Traceback (most recent call last): File setup.py, line 563, in module ext = get_extension() File setup.py, line 368, in get_extension ext_config = ExtensionConfiguration() File setup.py, line 65, in __init__ self.configure() File setup.py, line 93, in configure_unix CURL_CONFIG = scan_argv(--curl-config=, CURL_CONFIG) File setup.py, line 42, in scan_argv assert p, arg AssertionError: --curl-config= and this is why it should be arising: python setup.py build --with-ssl --curl-config=$CURL amp;amp; $CURL being empty. A local installation with the commands as in the tool_dependencies.xml doe generate $INSTALL_DIR/install-destination/bin/curl-config which should then be set to $CURL. Is there a way to check the logs, something I attempted by doing this: action type=shell_commandecho $INSTALL_DIR/action action type=shell_commandecho $CURL/action Or any alternate way to debug? On 29 April 2014 14:25, Saket Choudhary sake...@gmail.com wrote: Thanks Greg Bjoern, I get your point now. I will reconfigure my tool to take into account the other dependencies. Thanks once again, Saket On 30 April 2014 02:30, Greg Von Kuster g...@bx.psu.edu wrote: Hello Saket, I'm not a system-level expert, so please ignore my attempt at helping if it is incorrect. Your recipe for installing and compiling pycurl may be assuming that certain dependencies exist in the Galaxy environment into which it is being installed for testing, but they do not. Galaxy tools and tool dependency recipes can only assume the following dependencies are available in the Galaxy environment into which they will be installed (this list is available in the Tool Shed wiki on this page: https://wiki.galaxyproject.org/InstallAndTestCertification). In your case, a recipe should probably also be installing the libcurl-devel package (and possibly others??). Recipes need to be created for dependencies that are not on the following list, and then relationships can be defined between repositories that contain them and repositories that contain tools that depend upon them. The reason the following list is short is because starting up a new Galaxy instance should be as simple as cloning it and starting it up with run.sh. autoconf automake autotools-dev build-essential cmake git-core libatlas-base-dev libblas-dev liblapack-dev libc6-dev mercurial python2.6 python2.6-dev pkg-config subversion python-dev python-pip Greg Von Kuster On Apr 29, 2014, at 4:34 PM, Saket Choudhary sake...@gmail.com wrote: Hi Bjoern, There is no script installed, I generally just do this on my local system $ python setup.py build --with-ssl $ python setup.py install The documentation mentions the following options: PycURL Unix options: --curl-config=/path/to/curl-config use specified curl-config binary --openssl-dir=/path/to/openssl/dir path to OpenSSL headers and libraries --with-ssl libcurl is linked against OpenSSL --with-gnutls libcurl is linked against GnuTLS --with-nss libcurl is linked against NSS Saket On 29 April 2014 23:31, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Saket, is there any script installed with that package? --install-scripts may be needed. Also I'm wondering if there is no dependency on curl-lib? Cheers, Bjoern Am 29.04.2014 19:16, schrieb Saket Choudhary: Any comments on this? http://testtoolshed.g2.bx.psu.edu/view/saketkc/package_pycurl_7_19_3_1 On 17 April 2014 19:54, Saket Choudhary sake...@gmail.com wrote: My attempt to 'package' pycurl on testtoolshed fails with the following error: src/pycurl.c: In function ‘do_multi_info_read’: src/pycurl.c:3549:15: warning: call to ‘_curl_easy_getinfo_err_string’ declared with attribute warning: curl_easy_getinfo expects a pointer to char * for this info [enabled by default] src/pycurl.c: In function ‘do_curl_getinfo’: src/pycurl.c:2888:19: warning: call to ‘_curl_easy_getinfo_err_curl_slist’ declared with attribute warning: curl_easy_getinfo expects a pointer to struct curl_slist * for this info [enabled by default] error: could not create '/usr/local/share/doc': Permission denied A local install worked fine. Is this because of libcurl-devel missing on toolshed instance? ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Packaging pycurl on toolshed
Any comments on this? http://testtoolshed.g2.bx.psu.edu/view/saketkc/package_pycurl_7_19_3_1 On 17 April 2014 19:54, Saket Choudhary sake...@gmail.com wrote: My attempt to 'package' pycurl on testtoolshed fails with the following error: src/pycurl.c: In function ‘do_multi_info_read’: src/pycurl.c:3549:15: warning: call to ‘_curl_easy_getinfo_err_string’ declared with attribute warning: curl_easy_getinfo expects a pointer to char * for this info [enabled by default] src/pycurl.c: In function ‘do_curl_getinfo’: src/pycurl.c:2888:19: warning: call to ‘_curl_easy_getinfo_err_curl_slist’ declared with attribute warning: curl_easy_getinfo expects a pointer to struct curl_slist * for this info [enabled by default] error: could not create '/usr/local/share/doc': Permission denied A local install worked fine. Is this because of libcurl-devel missing on toolshed instance? ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Packaging pycurl on toolshed
Hi Saket, is there any script installed with that package? --install-scripts may be needed. Also I'm wondering if there is no dependency on curl-lib? Cheers, Bjoern Am 29.04.2014 19:16, schrieb Saket Choudhary: Any comments on this? http://testtoolshed.g2.bx.psu.edu/view/saketkc/package_pycurl_7_19_3_1 On 17 April 2014 19:54, Saket Choudhary sake...@gmail.com wrote: My attempt to 'package' pycurl on testtoolshed fails with the following error: src/pycurl.c: In function ‘do_multi_info_read’: src/pycurl.c:3549:15: warning: call to ‘_curl_easy_getinfo_err_string’ declared with attribute warning: curl_easy_getinfo expects a pointer to char * for this info [enabled by default] src/pycurl.c: In function ‘do_curl_getinfo’: src/pycurl.c:2888:19: warning: call to ‘_curl_easy_getinfo_err_curl_slist’ declared with attribute warning: curl_easy_getinfo expects a pointer to struct curl_slist * for this info [enabled by default] error: could not create '/usr/local/share/doc': Permission denied A local install worked fine. Is this because of libcurl-devel missing on toolshed instance? ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Packaging pycurl on toolshed
Hi Bjoern, There is no script installed, I generally just do this on my local system $ python setup.py build --with-ssl $ python setup.py install The documentation mentions the following options: PycURL Unix options: --curl-config=/path/to/curl-config use specified curl-config binary --openssl-dir=/path/to/openssl/dir path to OpenSSL headers and libraries --with-ssl libcurl is linked against OpenSSL --with-gnutls libcurl is linked against GnuTLS --with-nss libcurl is linked against NSS Saket On 29 April 2014 23:31, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Saket, is there any script installed with that package? --install-scripts may be needed. Also I'm wondering if there is no dependency on curl-lib? Cheers, Bjoern Am 29.04.2014 19:16, schrieb Saket Choudhary: Any comments on this? http://testtoolshed.g2.bx.psu.edu/view/saketkc/package_pycurl_7_19_3_1 On 17 April 2014 19:54, Saket Choudhary sake...@gmail.com wrote: My attempt to 'package' pycurl on testtoolshed fails with the following error: src/pycurl.c: In function ‘do_multi_info_read’: src/pycurl.c:3549:15: warning: call to ‘_curl_easy_getinfo_err_string’ declared with attribute warning: curl_easy_getinfo expects a pointer to char * for this info [enabled by default] src/pycurl.c: In function ‘do_curl_getinfo’: src/pycurl.c:2888:19: warning: call to ‘_curl_easy_getinfo_err_curl_slist’ declared with attribute warning: curl_easy_getinfo expects a pointer to struct curl_slist * for this info [enabled by default] error: could not create '/usr/local/share/doc': Permission denied A local install worked fine. Is this because of libcurl-devel missing on toolshed instance? ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Packaging pycurl on toolshed
Hello Saket, I'm not a system-level expert, so please ignore my attempt at helping if it is incorrect. Your recipe for installing and compiling pycurl may be assuming that certain dependencies exist in the Galaxy environment into which it is being installed for testing, but they do not. Galaxy tools and tool dependency recipes can only assume the following dependencies are available in the Galaxy environment into which they will be installed (this list is available in the Tool Shed wiki on this page: https://wiki.galaxyproject.org/InstallAndTestCertification). In your case, a recipe should probably also be installing the libcurl-devel package (and possibly others??). Recipes need to be created for dependencies that are not on the following list, and then relationships can be defined between repositories that contain them and repositories that contain tools that depend upon them. The reason the following list is short is because starting up a new Galaxy instance should be as simple as cloning it and starting it up with run.sh. autoconf automake autotools-dev build-essential cmake git-core libatlas-base-dev libblas-dev liblapack-dev libc6-dev mercurial python2.6 python2.6-dev pkg-config subversion python-dev python-pip Greg Von Kuster On Apr 29, 2014, at 4:34 PM, Saket Choudhary sake...@gmail.com wrote: Hi Bjoern, There is no script installed, I generally just do this on my local system $ python setup.py build --with-ssl $ python setup.py install The documentation mentions the following options: PycURL Unix options: --curl-config=/path/to/curl-config use specified curl-config binary --openssl-dir=/path/to/openssl/dir path to OpenSSL headers and libraries --with-ssl libcurl is linked against OpenSSL --with-gnutls libcurl is linked against GnuTLS --with-nss libcurl is linked against NSS Saket On 29 April 2014 23:31, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Saket, is there any script installed with that package? --install-scripts may be needed. Also I'm wondering if there is no dependency on curl-lib? Cheers, Bjoern Am 29.04.2014 19:16, schrieb Saket Choudhary: Any comments on this? http://testtoolshed.g2.bx.psu.edu/view/saketkc/package_pycurl_7_19_3_1 On 17 April 2014 19:54, Saket Choudhary sake...@gmail.com wrote: My attempt to 'package' pycurl on testtoolshed fails with the following error: src/pycurl.c: In function ‘do_multi_info_read’: src/pycurl.c:3549:15: warning: call to ‘_curl_easy_getinfo_err_string’ declared with attribute warning: curl_easy_getinfo expects a pointer to char * for this info [enabled by default] src/pycurl.c: In function ‘do_curl_getinfo’: src/pycurl.c:2888:19: warning: call to ‘_curl_easy_getinfo_err_curl_slist’ declared with attribute warning: curl_easy_getinfo expects a pointer to struct curl_slist * for this info [enabled by default] error: could not create '/usr/local/share/doc': Permission denied A local install worked fine. Is this because of libcurl-devel missing on toolshed instance? ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
